[Biopython-dev] Bio.Motif._Motif has_instances, has_counts

[Michiel de Hoon]

Hi Peter,

--- On Fri, 8/10/12, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > This means test_Tutorial.py is failing (across all
> platforms).
> > Presumably we would suggest switching these to
> somethinglike:
> >
> >     >>> arnt.instances is
> None
> >     False
> 
> Fixed:
> https://github.com/biopython/biopython/commit/b866e74dc9b6162517588ea4c0e4d1ecde5ed87c

Thanks for fixing this! Sorry I missed to do this when I was making these changes.

> Although since that won't work on old Biopython either
> (you'd
> get an AttributeError), perhaps we should label these new
> backwards compatible properties as obsolete with a pending
> deprecation warning for the next release (delay the
> deprecation)?
> 

I think we are being way too careful. Requiring proper deprecation warnings each time we make a change in Biopython will slow down its development and improvement. In the past when making changes to the existing code, we have gotten very few complaints; also in this case I doubt that anybody will miss has_counts, has_instances.

Best,
-Michiel.